Recent studies have elucidated host health implications of the bumble bee and honey bee (Family: Apidae) microbiome. However, less is known wild bee microbiomes, or microbiomes of non-corbiculate apids. Lactobacillus micheneri and its close relatives, L. timberlakei and L. quenuiae consistently associate with wild bees. Through bacterial genome sequencing, population genomics, bacterial 16S rRNA gene sequencing, culturing, and quantitative PCR, I studied the genetic capabilities, transmission mechanisms, and ecological interactions of the three lactobacilli species I refer to as the L. micheneri clade.

Bacterial genomes reveal potential functions while population and comparative genomics can identify important genes under selection to their hosts and environment. I sequenced 27 genomes from the L. micheneri clade and compared them to closely related, free-living and insect-associated Lactobacillus. I found that the L. micheneri clade has traits that imply adaptation towards the bees and flowers.

Transmission modes are important in maintaining microbial interactions between generations of hosts. To investigate transmission mechanisms of Lactobacillus micheneri to bees, I sequenced bacterial 16S rRNA gene to compare bacterial communities in overwintering leaf cutter bee nests and newly emerged bees. I found that L. micheneri survives over the winter but transmits to the next generation of bees rarely at best, and therefore appears to be preserved and transmitted elsewhere in the environment.

Lactobacilli can inhibit microorganisms in many human foods. Pollen provisions collected by bees are nutrient dense yet are normally not colonized with saprophytic fungi. Instead, Lactobacillus micheneri are abundant inside pollen provisions. I tested L. micheneri fungal inhibitory activity on plates and in sterilized pollen provisions. I found that while most L. micheneri strains can inhibit fungi, L. timberlakei is a strong fungal inhibitor on plates and in pollen provisions.

In this dissertation, I have contributed new knowledge and demonstrated that Lactobacillus micheneri is an interesting insect-associated symbiont. There are signatures of adaptation towards bees and flowers, and Lactobacillus are proven to inhibit microorganisms to the benefit of bees. However, while wild bee larvae benefit from L. micheneri’s ability to inhibit fungi, Lactobacillus micheneri does not readily vertically transmit and may be heavily reliant on horizontal transmission.

The honey bee, Apis mellifera, pollinates a wide variety of essential crops in numerous ecosystems around the world but faces many modern challenges. Among these, the microsporidian pathogen Nosema ceranae is one of the primary detriments to honey bee health. Nosema infects the honey bee gut, which harbors a highly specific, coevolved microbiota heavily involved in bee immune function and nutrition. Here, we extend previous work investigating interactions between the honey bee gut microbiome and N. ceranae by studying experimentally infected bees that were returned to their colonies and sampled 5, 10, and 21 days post-infection. We measured Nosema load with quantitative PCR and characterized microbiota with 16S rRNA gene amplicon sequencing. We found significant colony level variation in infection levels, and subtle differences between the microbiota of colonies with high infection levels versus those with low infection levels. Two exact sequence variants of Gilliamella, a core gut symbiont that has previously been associated with gut dysbiosis, were significantly more abundant in bees from colonies with high Nosema loads versus those with low Nosema loads. These bacteria deserve further study to determine if they facilitate more intense infection by Nosema ceranae.

Drought, rising temperatures, and expanding human populations are increasing water demands. Many countries are extending potable water supplies by irrigating crops with wastewater. Unfortunately, wastewater contains biologically active, long-lived pharmaceuticals, even after treatment. Run-off from farms and wastewater treatment plant overflows contribute high concentrations of pharmaceuticals to the environment. This study assessed the effects of common pharmaceuticals on a cosmopolitan saprophagous insect, Megaselia scalaris (Diptera: Phoridae). Larvae were reared on artificial diets spiked with contaminants of emerging concern (CECs) at environmentally relevant concentrations. Female flies showed no oviposition preference for treated or untreated diets. Larvae exposed to caffeine in diets showed increased mortality, and larvae fed antibiotics and hormones showed signs of slowed development, especially in females. The normal sex ratio observed in M. scalaris from control diets was affected by exposure to caffeine and pharmaceutical mixture treatments. There was an overall effect of treatment on the flies' microbial communities; notably, caffeine fed insects displayed higher microbial variability. Eight bacterial families accounted for approximately 95% of the total microbes in diet and insects. Our results suggest that CECs at environmentally relevant concentrations can affect the biology and microbial communities of an insect of ecological and medical importance.